[Bioperl-l] check for the continous segments to extract the sequences

Jason Stajich jason at bioperl.org
Thu Apr 26 21:54:59 EDT 2007


You want a connectivity algorithm.  One can be found on perlmonks.org  
as well as in Bio::Search::SearchUtils the method collapse_nums().  
You'll have to modify aspects of it to deal with ranges.

Good luck.
-jason
On Apr 26, 2007, at 6:29 PM, gopu_36 wrote:

>
> As a newbee to programming, thx for the support from this group.  
> Please
> ignore the message if this message is not relevant to this group as my
> problem may be a typical computer science recursive one! (as I am  
> not aware)
>
> I have an array like @array = (1, 1000, 1001, 2000, 4001, 5000,  
> 5001, 6000,
> 6001, 7000, 7001, 8000, 12001, 13000);
> The above array gives the posiiton of sequences like '1' shows the  
> start
> position and the second element '1000' gives the end of the  
> sequence and so
> on. All the even positions like 0,2,4... shows the starting points  
> of the
> sequence and odd positions like 1000, 2000, 5000 gives the END  
> positions of
> the sequences to be retrieved. basically I have to see whwther any  
> continous
> segments lie in the list and add them together to form a one whole  
> chunk.
> For example 1-1000 and 1001-2000 can be joined together to extract  
> sequences
> from 1-2000. In the same way 4001-8000 should be extracted and  
> 12001-13000
> and so on. As I said earlier, after checking the position, I will  
> be able to
> extract that part of sequence from a whole genome. Thanks for  
> taking ur
> time. Any tip or help would be greatly appreciated.
>
> Regards
> Gopu
> -- 
> View this message in context: http://www.nabble.com/check-for-the- 
> continous-segments-to-extract-the-sequences-tf3655281.html#a10211951
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/




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